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Antibody Structure

Antibody Structure

Overview
Antibodies, also known as immunoglobulins (Ig), are essential players of the adaptive immune system. These antigen-binding proteins are produced by B cells and make up 20 percent of the total blood plasma by weight. In mammals, antibodies fall into five different classes, which each elicits a different biological response upon antigen binding.
The Y-Shaped Structure of Antibodies Consists of Four Polypeptide Chains
Antibodies consist of four polypeptide chains: two identical heavy...

Antibody Structure and Classes

Antibody Structure and Classes

Antibodies, also known as immunoglobulins, are produced by B cells in response to foreign substances, such as bacteria and viruses. These proteins are critical for recognizing and neutralizing these substances, protecting the body from potential harm.
The basic structure of an antibody consists of four protein chains: two identical heavy chains and two identical light chains. These chains are held together by disulfide bonds and other non-covalent interactions, forming a Y-shaped structure.

Protein Organization

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence....

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Optimized Negative Staining: a High-throughput Protocol for Examining Small and Asymmetric Protein Structure by Electron Microscopy

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ABodyBuilder3: improved and scalable antibody structure predictions.

Henry Kenlay¹, Frédéric A Dreyer¹, Daniel Cutting¹

¹Exscientia, Oxford OX4 4GE, United Kingdom.

Bioinformatics (Oxford, England)

|October 4, 2024

Summary

ABodyBuilder3 enhances antibody structure prediction accuracy, particularly for CDR loops, using advanced language models. This improved model offers more reliable uncertainty estimation for antibody design.

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A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Area of Science:

Computational Biology
Structural Biology
Immunoinformatics

Background:

Antibody structure prediction is crucial for therapeutic development.
Existing models face challenges in accurately modeling CDR loops.
Scalable and accurate prediction tools are needed.

Purpose of the Study:

To introduce ABodyBuilder3, an advanced antibody structure prediction model.
To improve the accuracy of Complementarity-Determining Region (CDR) loop modeling.
To enhance the estimation of prediction uncertainties.

Main Methods:

Leveraging language model embeddings for enhanced prediction.
Implementing refined relaxation strategies for structural refinement.
Incorporating a predicted Local Distance Difference Test (pLDDT) for uncertainty quantification.

Main Results:

Achieved state-of-the-art accuracy in CDR loop modeling.
Demonstrated improved antibody structure prediction through advanced techniques.
Integrated pLDDT for reliable uncertainty estimation in predicted structures.

Conclusions:

ABodyBuilder3 represents a significant advancement in antibody structure prediction.
The model offers improved accuracy and uncertainty assessment for antibody design.
The software and model weights are publicly available for research use.